Dataset and code for the manuscript: You can bring plankton to fecal indicator organisms, but you cannot make them graze: particle contribution to E. coli and MS2 inactivation in surface waters

This deposit contains three elements: 1. data analysis code (.ipynb file); 2. code input files (data); and 3. code output files (figures and tables). The .ipynb file and dataset reproduce analysis, figures, and tables for the manuscript titled "You can bring plankton to fecal indicator organisms, but you cannot make them graze: particle contribution to E. coli and MS2 inactivation in surface waters." The experiments are described in the manuscript.

1. The data analysis code "2024_grazing_MS2_ecoli.ipynb" is a Jupyter Notebook in R and requires installation of an R kernel (installation instructions are available at: https://irkernel.github.io/installation/). To generate the figures and tables in the manuscript, place input files in a folder named "Data," create an empty folder named "Figures_and_tables", and execute the code in the same directory as the two created folders. These files are also available in github where the .ipynb file can be viewed directly (see "Links to related content" section).

2. The dataset includes eight code input files:
a. MS2 in experimental samples and controls quantified via plaque assay ("ms2.tsv")
b. E. coli in experimental samples and controls quantified via spread plate method ("ecoli.tsv")
c. absorbance spectra of water samples ("abs.csv"),
d. DAPI cell counts in raw water (DAPI.csv)
e. field data for water samples (i.e., date, time, temperature, salinity, pH, turbidity), the amount of raw water filtered to enumerate plankton, the volume of ethanol used to preserve plankton, the amount of raw water filtered for ~500% concentration ("c1"), and the amount of raw water filtered for ~1000% concentration ("c2") ("field.csv)
f. total solids data in the raw water ("solids.csv")
g. zooplankton enumeration in undiluted ethanol (zoo1.csv)
h. zooplankton enumeration in diluted ethanol (zoo2.csv)

3. The dataset contains figures and tables generated by the code and referenced in the manuscript (.jpg and .doc files).